Score 1 fresh pomegranate and place in a bowl of water. Break open the pomegranate under water to free the arils (seed sacs). The arils will sink to the bottom of the bowl and the membrane will float to the top. Sieve and put the arils in a separate bowl. Reserve ¼ cup of the arils from fruit and set aside. (Refrigerate or freeze remaining arils for another use.)
Prepare fresh pomegranate juice.(See note)
In a 6-quart saucepan or Dutch oven, combine pomegranate juice, lemon juice and pectin. Over high heat, bring mixture to a boil.
Stir in sugar all at once, then stir constantly. Heat mixture again until it comes to a full rolling boil; boil 1 minute over medium-high heat.
Remove from heat and skim foam from jelly with a spoon. Discard foam.
Immediately ladle the jelly into clean jelly jars with lids or refrigerator containers with tight-fitting lids. Sprinkle reserved arils over the top of each container of jelly. Cover tightly. Let stand for 45 minutes to cool, then refrigerate for 1¼ hours. If not using immediately, refrigerate for up to 4 to 6 weeks or freeze for up to 1 year.
For 2 cups of juice, cut 4—6 large pomegranates in half and juice them with a citrus reamer or juicer. Pour mixture through a cheesecloth-lined strainer or sieve. Set the juice aside.